Hi Ariel,
One solution is that you use the development version of Bioconductor
(BioC 2.5, to be released soon, based on the R-2.10 series).
In the development version of genefilter it looks like the nsFilter()
function has been improved in order to deal properly with the
peculiarity of the ath1121501.db package. Internally it's now
calling a little helper function .findCentralID() (not exported)
in order to determine what's the central ID in the annotation
package:
library(genefilter)
library(hgu95av2.db)
library(ath1121501.db)
> genefilter:::.findCentralID("hgu95av2")
[1] "ENTREZID"
> genefilter:::.findCentralID("ath1121501")
[1] "ACCNUM"
Cheers,
H.
Ariel Chernomoretz wrote:
> Hi all,
> I am currently analyzing some arabidopsis thaliana experiments (ath1121501
> GeneChip)
> The corresponding annotation package, ath1121501.db, is a little bit
> 'special' as
> there is no ENTREZID map for the chip.
> I would like to cheat and create a fake ath1121501ENTREZID for the
> environment as a copied instance of ath1121501ACCNUM (in order to use, for
> instance, the genefilter package's function "nsFilter" to deal with non
> annotated, or duplicated probesets)
>> The problem is that I am not able to create a new entry in the
> package:ath112150.db as it is a locked environment. Is there any way to
> temporarily unlock it, do some stuff and lock it again?
> (It seems easy to lock environments, using the lockEnvironment function, but
> I did not find an easy way to unlock them)
>> Thanks in advance
> Ariel./
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
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